This project addresses the looming optical detection bottleneck in sequencing by developing an ultra high-throughput 250nm-scale optical scanner. In addition to a 50X gain in throughput, the approach also supports a 4X feature-size reduction path that can help drive down reagent usage by a factor of 16X. Together, these throughput and density gains provide the needed instrument-side support in the push to break the $1,000 genome barrier. The approach is based on a novel imaging technique called Synthetic Aperture Optics (SAO) that allows a high-resolution image to be reconstructed from a series of low-resolution samples. In this manner, a SAO scanner trades off expensive, time-intensive stage movements with relatively fast imaging samples. Another advantage of SAO is that the number of samples can be dynamically adjusted as the demand for resolution increases or decreases. This fundamental property of SAO allows superior resolution over conventional light microscopy, as well as significantly higher scanning throughput. This project intends to develop a commercially viable prototype SAO scanner and verify its accuracy and throughput by sequencing an ePCR-amplified genomic reference library on 250nm-scale beads. The scanner can potentially be integrated with a range of chemistries and can be used both for de novo sequencing and for re-sequencing. The success of this project will enable the industry to fully exploit gains in sequencing chemistries to drive reagent, instrument, and operation costs down below the $1,000 genome target. PUBLIC HEALTH RELEVANCE: This project aims to develop an advanced optical detection technology that will significantly lower the cost of DNA sequencing. This cost reduction will drive innovation in basic research, drug development, and medical diagnostics.